BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714062.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 328,750 number of mapped reads = 231,745 (70.49%) number of supplementary alignments = 7,978 (2.43%) number of secondary alignments = 0 number of mapped bases = 29,708,813 bp number of sequenced bases = 29,128,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,060 duplication rate = 42.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.2362 >>>>>>> ACTG content number of A's = 8,104,941 bp (27.82%) number of C's = 6,148,567 bp (21.11%) number of T's = 7,678,674 bp (26.36%) number of G's = 7,196,091 bp (24.7%) number of N's = 164 bp (0%) GC percentage = 45.81% >>>>>>> Mismatches and indels general error rate = 0.0429 number of mismatches = 1,141,998 number of insertions = 33,814 mapped reads with insertion percentage = 14.11% number of deletions = 98,796 mapped reads with deletion percentage = 40.6% homopolymer indels = 28.22% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 1.312X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2531393 0.010156014816909925 1.0513335921745413 chr2 243199373 3318959 0.013647070545695856 3.3158284120025994 chr3 198022430 1595936 0.008059369840073168 0.7364790281797249 chr4 191154276 1472776 0.007704645853697774 0.8409906816762462 chr5 180915260 1618342 0.008945304005864404 0.8570719582785776 chr6 171115067 1170898 0.006842752193177705 0.6640884265358961 chr7 159138663 1259232 0.007912797407377992 0.8155939841287564 chr8 146364022 1478208 0.010099531153906115 1.1255590866127823 chr9 141213431 1094130 0.007748059035545989 0.8469457714028216 chr10 135534747 1533380 0.011313556367947475 0.9535987255044646 chr11 135006516 1421707 0.01053065468336358 1.1738433324633868 chr12 133851895 1171042 0.008748789100072136 0.8909916701393954 chr13 115169878 862816 0.007491681114744257 0.8476291613191088 chr14 107349540 985198 0.009177477611920833 1.082120950468989 chr15 102531392 781353 0.007620622179790556 0.729342303622216 chr16 90354753 977938 0.010823315515012253 1.0731246755965533 chr17 81195210 965687 0.011893398637678257 1.2250616047357479 chr18 78077248 705553 0.009036601802358608 0.7744561923367086 chr19 59128983 563073 0.009522791893782445 1.1556667507411553 chr20 63025520 788382 0.012508932889407338 1.0955092079481283 chr21 48129895 271573 0.0056425014016756115 0.6431449870542113 chr22 51304566 327608 0.006385552506184343 0.7841437721245937 chrMT 16571 190188 11.477158892040311 104.53934046744205 chrX 155270560 2503306 0.01612221917664237 1.09954293933913 chrY 59373566 120135 0.002023375183494958 0.353547964671787